In Linux the JACK 'system' inputs and outputs are limited to what you physically have on your soundcard, but inputs and outputs of the software that connects to JACK are controlled by said software.
In the preferences in PD you can specify how many input and output channels you want PD to use.These channels will show up in the JACK patchbay under 'puredata'.
The DAW that I use is Ardour, and when you add tracks in the program, those channels show up in the JACK patchbay. Each track will get an input and an output that can be connected to the input or output of another program. In this case you want your outputs from puredata to connect to the inputs of the individual tracks in Ardour.
If you don't see the inputs and outputs from puredata or your DAW in the JACK patchbay then:
- your software is not connecting to JACK...it's probably connecting directly to ALSA
or
- you are starting the software before you start JACK, in which the software isn't getting registered with JACK, and JACK can't manage the connections.
I'll make some screenshots for you if that will help